tbuckley/cabot-search huggingface dataset:
EPCO-03. PATHWAY-BASED STRATIFICATION OF GLIOBLASTOMA BY MULTI-OMICS INFORMS SUBTYPE-SPECIFIC MASTER KINASES-PHOSPHOSITE SUBSTRATES
Authors: Simona Migliozzi, Young Taek Oh, Mohammad Hasanain, Luciano Garofano, Fulvio D'Angelo, Alberto Picca, Franck Bielle, Jann Sarkaria, Michele Ceccarelli, Marc Sanson, Anna Lasorella, Antonio Iavarone
Journal: Neuro-Oncology (2022)

Abstract Tumor heterogeneity and broad therapeutic resistance are major challenges when treating patients with glioblastoma (GBM). Moreover, different from other cancer types, the absence of clinically useful classifiers for glioblastoma has hampered the translation of genomic and proteomic information to improve diagnosis and design precision therapeutics for patients. We analyzed a large dataset of human GBM to determine the multi-omics features characterizing the four GBM subtypes that we have recently identified through single-cell RNA sequencing and validated in bulk tumor analysis. Each subtype exhibits activation of unique functional traits that confer distinct therapeutic vulnerabilities. The examination of proteomics, phosphoproteomics, metabolomics, lipidomics and acetylomics data revealed that each GBM subtype has a coherent molecular structure driving the dominant function traceable in each analytical platform. Functional classes are not a specific attribute of GBM as we identified the same subtypes in breast and lung cancer. To test the translational impact of proteomic data in GBM, we developed an unbiased protein kinase signaling network approach for the selection of master kinases (MKs) aberrantly activated in each GBM subtype. We identified therapeutically actionable MKs and novel phosphorylation substrates that we experimentally validated. To provide rapid translation of the functional classifier for precision medicine in GBM, we developed a probabilistic classification tool which determines the probability that a patient’s GBM belongs to one of the four subtypes, exhibiting optimal performance when using RNA extracted from either frozen and paraffin-embedded tissues. The algorithm is publicly accessible and can be used to evaluate the association of therapeutic response with GBM subtypes and as tool for selection criteria in prospective clinical trials.
IMMU-26. HEIGHTENED LEVELS OF CIRCULATING CELL-FREE DNA CONTRIBUTE TO PERIPHERAL IMMUNOSUPPRESSION DURING GBM PROGRESSION
Authors: Katayoun Ayasoufi, Delaney Wolf, Zachariah Tritz, Lauren Gulbicki, Fang Jin, Michael Hansen, Cori Fain, Aaron Johnson
Journal: Neuro-Oncology (2022)

Abstract Glioblastoma (GBM) is an incurable and aggressive form of brain cancer that is associated with severe peripheral immunosuppression. This immunosuppression is a critical barrier to patient survival and the success of immune modulatory therapies. Using the murine GL261 model of GBM, we recapitulated major features of peripheral immunosuppression observed in patients including T cell lymphopenia. We determined that peripheral immunosuppression in GBM is multifaceted and involves release of novel non-steroidal soluble factors with large molecular weight that are found in sera of glioma-bearing mice. These high molecular weight species potently inhibits T cell proliferation in vitro despite the presence of strong T cell stimulation. Our goal was to determine the identity of the immunosuppressive species in serum of glioma-bearing mice. We performed state-of-the-art comparative high throughput mass spectrometry on fractionated and multiplexed sera isolated from control and glioma-bearing mice. This proteomics analysis demonstrated histones as a top highly abundant protein in serum of glioma-bearing mice compared to naïve controls. Cell-free DNA has been recently identified as an immune suppressive factor in circulation and can be bound to histones. We, therefore, assessed cell-free DNA levels in the serum of glioma-bearing mice. We determined that sera isolated from glioma-bearing mice harbor significantly higher concentrations of double stranded and single stranded cell-free DNA compared to healthy controls. Reducing the DNA content in serum, using DNAse treatment, partially improved the defect in T cell proliferation observed when T cells are exposed to serum isolated from glioma-bearing mice. These data indicate that heighted levels of circulating DNA in serum contributes to peripheral immunosuppression in GBM. These findings provide a tractable approach to investigate the cellular source and immunosuppressive effects of cell-free DNA in murine models of GBM and to devise strategies to reverse immunosuppression with the hope of improving outcomes in patients.
BIOM-27. PROGNOSTIC SIGNIFICANCE OF EXTENT OF RESECTION IN GLIOMA ACCORDING TO THE 2021 WHO CLASSIFICATION
Authors: Kuniaki Saito, Yuta Sasaki, Saki Shimizu, Jun Nagai, Yuki Yamagishi, Nobuyoshi Sasaki, Keiichi Kobayashi, Yoshiaki Shiokawa, Hirofumi Nakatomi, Motoo Nagane
Journal: Neuro-Oncology (2022)

Abstract BACKGROUND In the updated 2021 WHO classification, diffuse gliomas were strictly reclassified by molecular statuses. In glioblastoma (GBM), the prognostic significance of the resection has been shown, but the excision rate to be achieved in the new classification has not been defined. Moreover, the correlation between the extent of resection (EOR) and the prognosis is still controversial for other gliomas. METHODS IDH 1/2 mutations and TERT promoter mutations were analyzed by Sanger sequencing, 1p/19q co-deletion by microsatellite or MLPA, and EGFR amplification and CDKN2A deletions by MLPA. The correlation between the resection rate and prognosis of each tumor type in the 2021/2016 WHO classification was analyzed retrospectively. RESULTS According to the 2021 classification, 293 patients with GBM, IDH-wild type, 68 with astrocytoma, IDH-mutant (2/3/4 22/26/20), and 58 with oligodendroglioma, IDH-mutant and 1p/19q co-deleted were identified. Based on the 2016 classification, they were diagnosed as 314 GBM, 106 astrocytoma (Gd II/III 37/69), and 59 oligodendroglioma. For GBM, IDH-wild type (2021 classification), a prolonged OS benefit was observed with &amp;gt;25% removal (p=0.042), whereas, more than 20% of tumor removal for patients with GBM (2016 classification) resulted in OS prolongation. EOR was a significant favorable prognostic factor for grade II/III astrocytoma by the 2016 classification, but not for astrocytoma, IDH-mutant (grade 2/3) in the 2021 classification. When analyzed only in patients with astrocytoma, IDH-mutant by the 2021 classification, EOR was not significantly prognostic, suggesting that poorer prognosis of patients with unresectable IDH-wild type astrocytomas (2016 classification) might have a negative impact on the outcome. CONCLUSION There was a strong correlation between EOR and prognosis in patients with GBM, and &amp;gt;25% removal was considered significant according to the 2021 classification. For astrocytoma in the 2021 classification, EOR did not show a prognostic significance, but further validation including grading effect is warranted.
EPID-08. AGE-STRATIFIED SURVIVAL ANALYSES OF PHARMACOLOGICAL TREATMENTS IN PATIENTS WITH GLIOBLASTOMA
Authors: Erik Rabin, Xinlei Mi, Jonathan Huang, Miri Kim, Andreas Mozny, Christina Amidei, Erica Sieg, April Bell, Lijie Zhai, Prashant Bommi, Kristen Lauing, Rimas Lukas, Derek Wainwright
Journal: Neuro-Oncology (2022)

Abstract Glioblastoma is the most common primary malignant brain tumor in adults. Age is a prognostic factor for grade IV glioma (GIV) survival, where older adults 65 and older, tend to have quicker mortality compared to adults 18-64. This may be due to intrinsic aspects of the aged host, including age-dependent changes to the brain and immune systems. We studied pharmacologic management of GIV patients treated with medications affecting the brain, immune, and other systems for associations with age and survival. Electronic records for 1,208 GIV patients were collected at a single institution from 1/1/2000 to 9/8/2021 and used to construct a multivariable time-dependent cox model that examined intra-cohort hazards associated with 14 different categories of outpatient medications. Date of diagnosis was identified as the start-time and subject death was used to define the event-time. Patients who were alive or lost to follow-up were censored to last recorded date. Survival time was calculated as the difference between diagnosis date and event time or censorship. For positive control, we confirmed that younger and older patients experienced an improved hazard with temozolomide. Strikingly, younger, but not older patients, experienced increased hazard with a steroid prescription (1.46 [1.12,1.90], **). In contrast, older, but not younger patients experienced improvements in hazard with prescription of neurological medications including benzodiazepines (0.47 [0.27, 0.80] **) and anti-convulsants (0.28 [0.08, 0.90] *), in addition to heart failure treatments including angiotensin II inhibitors (0.48 [0.27, 0.85] *) and diuretics (0.30 [0.15, 0.87] *). Patients prescribed antidepressants didn’t show improved hazard across younger and older GIV patients, which consistent with our previously published work. These data indicate novel associative benefits due to prescription of select pharmacologic agents that vary with patient age. This work may be used to better understand therapeutic approaches that selectively benefit younger vs. older adults with GIV.
EPCO-02. GENOME-WIDE DNA METHYLATION PROFILING AND GENETIC CHARACTERIZATION OF LONG-TERM SURVIVAL IDH WILD-TYPE GLIOBLASTOMA PATIENTS
Authors: Evelina Miele, Elisabetta Lazzarini, Andrea Ciolfi, Lucia Pedace, Claudia Nardini, Sara Patrizi, Angela Mastronuzzi, Marco Tartaglia, Elena Anghileri, Chiara Calatozzolo, Elena Antonia Lamperti, Monica Patanè, Franco Locatelli, Stefano Indraccolo, Bianca Pollo
Journal: Neuro-Oncology (2022)

Abstract Glioblastoma multiforme (GBM) has a dismal outcome of approximately 12 months. Less than 5% of patients (long-term survivors-LTS) survives more than 5-years, including IDH-mutant gliomas. Nevertheless, the molecular fingerprint of LTS remains largely uncharted. DNA methylation (DNAm) is an epigenetic modification, altered in cancer and used to classify brain tumors. In this multicentric study sponsored by Alleanza Contro il Cancro (ACC) network, we aimed to molecularly characterize LTS vs standard survival GBM (CTR) by DNAm/Copy Number Variation (CNV) and mutation profiling. We analyzed 51 IDHwt GBM samples (27LTS/24CTR) by Illumina EPIC beadChip and AmpliSeq Comprehensive Cancer Panel. We ran methylation data through the brain tumor classifiers v11b4 and v12.5, performed multidimensional scaling analysis and investigated differentially methylated regions (DMR) correlating them with survival. According to v11b4, cases were classified as: 43 GBM IDHwt (22LTS/21CTR), 27 with a calibrated score &amp;gt;0.84 (16LTS); Plexus Tumor with low scores (2LTS/3CTR); 3 LTS samples did not match. A diagnostic refinement was observed by the v12.5, with 48 cases classifying as GBM IDHwt (25LTS/23CTR) and 35 (19LTS) with optimal score. The LTS group was more heterogeneous, with 4 cases matching in the pedHGG subtypes, including 2 cases in young adults, one with high tumor mutational burden and MSH6 mutation. No specific DNAm genomic profile was observed for LTS patients but we identified 18 significant DMRs, 4 associated with survival probability. At CNV analysis, most cases showed classical alterations (Chr7 gain with or w/o EGFR amplification, 9p21 loss, Chr10 loss) while pedHGG were associated with PDGFRA amplification, 1q gain, 13q loss. NGS identified at least 1 pathogenic variant in 40 cases (22CTR/18LTS) and showed a higher prevalence of mutation negative cases among LTS. No significant difference between the 2 groups was observed in terms of prevalence of mutated genes or number of VUS per sample.
EPCO-10. SYSTEMS BIOLOGY-BASED THERAPEUTIC PREDICTIONS WITH GBMSYGNAL AND CLINICAL CORRELATES IN THE REAL-WORLD LONGITUDINAL OUTCOMES REGISTRY XCELSIOR
Authors: Timothy Stuhlmiller, Serdar Turkarslan, Julie Friedland, Mark Shapiro, Santosh Kesari, Anoop Patel, Nitin Baliga
Journal: Neuro-Oncology (2022)

Abstract Glioblastoma is an aggressive disease with multiple disrupted signaling networks in the same tumor, demanding the development of personalized combination regimens. Using SYstems Genetics Network AnaLysis we analyzed TCGA multiomics datasets for 422 glioblastoma patients to generate a predictive disease network model (gbmSYGNAL). This model seeks to uncover how subsets of mutations causally modulate regulators (transcription factors, miRNAs, etc.) that mechanistically regulate gene modules (“regulons”) associated with disease progression. Using the real-world registry XCELSIOR (NCT03793088), we identified 55 anti-cancer therapies utilized in glioblastoma treatment (N = 354 patients) and associated them with positive or negative regulon activity within individual patients across the TCGA cohort. A median of 12 regulons were targeted by each drug. Interestingly, nilotinib targeted only 5 regulons but they were found to be active in 38% of patients and regulons overactive in &amp;gt;35% of patients were targeted by repurposed anti-cancer drugs including celecoxib, hydroxychloroquine, and tocilizumab. Standard-of-care treatments lomustine and bevacizumab were predicted to be active in only 28% and 23% of patients, respectively. Using gbmSYGNAL, we then prioritized drugs for 12 additional patients from the XCELSIOR registry. Median overactive regulons per patient was 110 (range 55-254) represented by a median 28 molecular targets (range 17-37). Surprisingly, regulons targeted by metformin were predicted to be overactive in all patients. Certain regulons displayed a binary pattern (high “on” activity or completely “off” per patient) including those targeted by pemetrexed, pembrolizumab, and valproic acid while others showed a gradient of activity across patients including selinexor, panobinostat, palbociclib, and alpelisib. Systems biology analysis of commercially available NGS data combined with the XCELSIOR direct patient engagement platform yielded therapeutically actionable insights for glioblastoma patients in real time. Correlation with clinical outcomes is ongoing for ~50 additional patients and will be presented at the meeting.
DDDR-28. EGFR AND SRC-MEDIATED ACTIVATION OF STAT3 DRIVES RESISTANCE TO MITOTIC INHIBITORS IN GLIOBLASTOMA, AND CAN BE REVERSED WITH FDA-APPROVED DRUGS
Authors: Rajappa Kenchappa, Athanassios Dovas, Michael Argenziano, Christian Meyer, Lauren Stopfer, Matei Banu, Brianna Pereira, Jessica Griffith, Afroz Mohammad, Surabhi Talele, Natanael Zarco, William F Elmquist, Forest White, Vito Quaranta, Peter Sims, Peter Canoll, Steven Rosenfeld
Journal: Neuro-Oncology (2022)

Abstract While the allure of targeted therapies in oncology has been their high degree of specificity and potency for key tumor drivers, they have been disappointing in glioblastoma (GBM), even for drugs that are blood brain barrier permeable and CNS retained. This point is highlighted by the experience with mitotic spindle inhibitors, drugs which block the G2M transition and induce mitotic catastrophe—a phenotype characterized by cell enlargement and polyploidy that leads to apoptotic cell death. We have shown that one of these, a potent inhibitor of the mitotic kinesin Kif11 (ispinesib), is highly active against GBM tumor initiating cells and prolongs survival in murine models of this disease. However, tumors eventually progress, reflecting the development of drug resistance. Although ispinesib resistant GBM cells develop mitotic catastrophe, they become highly resistant to the apoptosis that typically follows and continue to proliferate. We find that this apoptosis resistance requires phosphorylation of the transcription factor STAT3 at two residues—Y705 and S727. Phosphorylation of Y705, mediated by SRC kinase, translocates STAT3 to the nucleus where it induces transcription of anti-apoptotic proteins. Phosphorylation at S727, mediated by EGFR, translocates STAT3 to the mitochondria where it blocks release of cytochrome c—the penultimate effector in apoptosis. Simultaneously inhibiting both SRC and EGFR with FDA-approved, CNS permeant inhibitors reverses this resistance and significantly prolongs survival in ispinesib-treated GBM-bearing mice. Furthermore, we find that resistance to several other mitotic inhibitors also utilizes this STAT3-driven mechanism and can likewise be reversed with combined EGFR and SRC inhibition. Thus, our work demonstrates how a promising therapeutic approach, which has been disappointing in GBM, can in fact be rendered effective by anticipating and prospectively treating ab initio the mechanism that drives treatment resistance.
EPCO-13. IDENTIFYING REGULATORS OF GLIOMA CELL STATE DIVERSITY AND EVOLUTION VIA JOINT SINGLE NUCLEUS RNA AND CHROMATIN ACCESSIBILITY
Authors: Kevin Johnson, Kevin Anderson, Djamel Nehar-Belaid, Frederick Varn, Amit Gujar, Elise Courtois, Paul Robson, Hyo-Eun Moon, Anna Golebiewska, Sun Ha Paek, Simone Niclou, Roel Verhaak
Journal: Neuro-Oncology (2022)

Abstract Glioma cellular heterogeneity and plasticity represent fundamental obstacles to effective therapies. Understanding the determinants that govern glioma cell diversity and adaptability is critical to overcoming treatment resistance. Recent single cell DNA methylation studies have demonstrated that dynamic epigenetic alterations facilitate glioma cell state shifts and stress response. However, information regarding other modes of epigenetic gene regulation, such as chromatin accessibility, and how therapy shapes cellular heterogeneity remains limited. To determine the critical regulators of glioma cell state plasticity under treatment, we profiled 36 tumors (n = 23 adult patients) with joint single nucleus RNA and ATACseq including 13 longitudinal initial – recurrent pairs that yielded a total of 79,945 cells (37,883 malignant cells). We identified chromatin peaks that were uniquely open in glioma cells (n = 14,462 peaks, FDR &amp;lt; 0.05) compared with tumor microenvironmental cells including neuronal, perivascular, glial, and immune populations. Among malignant cells, differentiated-like cells exhibited more recurrent regions of accessibility than stem-like cells. These populations could be further delineated by differential peak enrichment of transcription factor binding sites in the stem-like (TCF12, ASCL1), differentiated-like (SMARCC1, JUN), and proliferating stem-like (E2F4) malignant cells nominating these transcription factors as master regulators. We confirmed that these cell state-specific open chromatin peaks overlapped enhancer regions via single nucleus multiomics and bulk H3K27ac profiling in 3 patient-derived cell lines. We further demonstrated that there are cell state-specific chromatin changes at recurrence with a trend toward a more open chromatin state that was associated with coordinated transcriptional changes. Finally, we incorporated matched longitudinal whole genome sequencing data to evaluate mutational profiles and differentiate between predominantly epigenetically driven changes and epigenomic co-evolution with the genome. Together, these findings define the key epigenetic switches that shape glioma cell states and facilitate plasticity during tumor progression.
EPID-24. TIMING OF STANDARD-OF-CARE CHEMO-RADIATION THERAPY FOLLOWING SURGICAL RESECTION OR STEREOTACTIC BIOPSY
Authors: Ping Zhu, Clark Chen
Journal: Neuro-Oncology (2022)

Abstract OBJECT The literature examining the optimal timing for initiating post-surgical therapy after glioblastoma surgery is brimming with inconsistencies, with reports of both deleterious effects and benefits in the delay of post-surgical therapy at various time intervals. Moreover, there is currently limited data pertinent to the post-Stupp regimen era. Here, we use the National Cancer Database (NCDB) to explore this matter, with a focus on patients who underwent the standard-of-care (SOC) Stupp regimen. METHODS The study cohort included newly glioblastoma patients from the NCDB, with exclusion of patients age &amp;lt; 40 [as proxy for isocitrate dehydrogenase (IDH) mutated astrocytoma] and stratified for Methyl-guanine-methyl transferase (MGMT) promotor methylation. Timing of initiating SOC was grouped by 0-2, 2-4, 4-6, 6-8, and &amp;gt; 8 weeks from surgery. Biopsy and craniotomy patients were analyzed separately. The Kaplan-Meier method and Cox proportional hazards regression were applied for survival analysis. RESULTS We identified 6511 glioblastoma patients who underwent SOC therapy with available MGMT methylation status. SOC was initiated in 228 (3.5%), 2478 (38.1%), 2954 (45.4%), 646 (9.9%), and 205 (3.2%) patients at 0-2, 2-4, 4-6, 6-8, and &amp;gt;8 weeks after surgery. For craniotomy patients, initiation of SOC at 0-2 weeks was associated with an increased risk of death relative to SOC initiation at 4-6 weeks (HR: 1.19, p = 0.036). These results remain robust after controlling for the extent of resection, tumor size, and tumor location (HR: 1.19, p = 0.044). Such association was not observed in patients who underwent stereotactic biopsy (HR: 1.27, p = 0.148). Patients who received SOC at 6-8 weeks post-craniotomy (HR: 0.96, p = 0.420) or biopsy (HR: 0.93, p = 0.628) did not appear to worsen survival outcomes. CONCLUSION Optimal timing for initiation of SOC differ for craniotomy and needle biopsy patients. Initiating SOC within 2 weeks after craniotomy could lead to worse survival outcomes for GBM patients.
DISP-08. DISPARITY OF RADIATION TREATMENT AND CLINICAL OUTCOME AMONG ADULT MEDULLOBLASTOMA PATIENTS
Authors: Kailin Yang, Mina Dinh, Kireem Nam, Sanjana Madishetty, Sarah Kilic, Jacob Scott, Samuel Chao, Erin Murphy, John Suh
Journal: Neuro-Oncology (2022)

Abstract OBJECTIVES Medulloblastoma is the most common malignant pediatric brain neoplasm, but its pattern of care among adult patients has not been standardized. Disparity in socioeconomic factors influence treatment decision and prognosis in many cancers. This study aims to analyze the impact of insurance and socioeconomic status on the clinical outcome of adult patients with medulloblastoma in the United States. METHODS Adult patients (age 18 or older) with medulloblastoma in the brain diagnosed from 2004 to 2016 were identified from the National Cancer Database (NCDB). OS was evaluated with the Kaplan-Meier and Cox proportional hazards methods. Logistic regression was performed to assess the effect on dichotomized dependent variable. RESULTS A total of 1,282 adult patients with medulloblastoma were identified. The mean age was 29 years (range 18-85). 30.9% of patients were uninsured or had Medicaid, 83.2% were white, 81.9% received radiation therapy, and 59.9% received chemotherapy. Using univariate analysis, insurance status, radiation, and chemotherapy were statistically associated with OS. Uninsured/Medicaid patients were associated with poorer OS (HR 1.36, 95% CI 1.08-1.71, p &amp;lt; 0.01) compared to those with private insurance. Treatment with radiation therapy (HR 0.43, 95% CI 0.34-0.55, p &amp;lt; 0.01) or chemotherapy (HR 0.51, 95% CI 0.41-0.62, p &amp;lt; 0.01) portended improved OS. After adjusting for age, sex, race, and Charlson-Deyo comorbidity score, statistically significant differences in OS were seen for patients with no insurance/Medicaid. Using multivariate logistic regression, patients with either no insurance or Medicaid were less likely to receive radiation therapy (OR 0.69, 95% CI 0.51-0.95, p = 0.02) compared to patients with private insurance. CONCLUSION Using a large national cohort of adult medulloblastoma patients, this study demonstrated the statistically significant disparity of patient outcomes with insurance status. An effort to address healthcare disparity and increase access to cancer care may improve the clinical outcome for adult patients with medulloblastoma.